Change Log¶
All notable changes to this project are documented in this file. This project adheres to Semantic Versioning.
Unreleased¶
Changed¶
- Use pigz for output file compression in
bbduk-single
andbbduk-paired
processes - Use
resolwebio/rnaseq:4.9.0
Docker image in processesbbduk-single
,bbduk-paired
,trimmomatic-single
,trimmomatic-paired
,alignment-bowtie
,alignment-bowtie2
,alignment-hisat2
,alignment-subread
,cuffmerge
,pca
,cuffdiff
,differentialexpression-edger
,cufflinks
,cuffnorm
,cuffquant
,expression-aggregator
,htseq-count
,htseq-count-raw
,index-fasta-nucl
,rsem
,upload-bam
,upload-bam-indexed
,upload-bam-secondary
,upload-expression
,upload-expression-cuffnorm
,upload-expression-star
,upload-genome
,upload-gaf
,upload-obo
,upload-fasta-nucl
,regtools-junctions-annotate
,cutadapt-custom-single
,cutadapt-custom-paired
,bam-split
,gff-to-gtf
,spikein-qc
,differentialexpression-shrna
,feature_counts
,salmon-index
,salmon-quant
,library-strandedness
,qorts-qc
,alignment-star
,alignment-star-index
,cutadapt-3prime-single
,cutadapt-single
,cutadapt-paired
,differentialexpression-deseq2
,stringtie
,cutadapt-corall-single
,cutadapt-corall-paired
,umi-tools-dedup
,shrna-quant
. - Use
resolwebio/common:1.3.1
Docker image in processesamplicon-table
,mergeexpressions
,upload-bedpe
,upload-bam-scseq-indexed
,upload-diffexp
,upload-etc
,upload-sc-10x
,upload-multiplexed-single
,upload-multiplexed-paired
,archive-samples
,samtools-idxstats
,seqtk-sample-single
,seqtk-sample-paired
,basespace-file-import
,clustering-hierarchical-samples
,clustering-hierarchical-genes
,import-sra
,import-sra-single
,import-sra-paired
.
Fixed¶
- Fix Mapping search for
source_id
/target_id
25.1.0 - 2020-01-14¶
Added¶
Changed¶
- Extend the MultiQC report so that the Sample summary table is created for the compatible Data objects
- Bump CPU and memory requirements for the
alignment-bowtie2
process - Move upload test files of differential expression to its own folder
Fixed¶
- Fix typo in
scheduling_class
variable in several Python processes - Handle cases of improper tags passed to
read_group
argument of thebqsr
process - When processing differential expression files, a validation is performed for numeric columns
25.0.0 - 2019-12-17¶
Added¶
- Add
alleyoop-rates
process - Add
alleyoop-utr-rates
process - Add
alleyoop-summary
process - Add
alleyoop-snpeval
process - Add
alleyoop-collapse
process - Add
slam-count
process - Add
workflow-slamdunk-paired
workflow
Changed¶
- BACKWARD INCOMPATIBLE: Refactor
slamdunk-all-paired
process to support genome browser visualization and add additional output fields - Append sample and genome reference information to the summary output
file in the
filtering-chemut
process - Bigwig output field in
bamclipper
,bqsr
andmarkduplicates
processes is no longer required - Support Slamdunk/Alleyoop processes in MultiQC
- Enable sorting of files in
alignment-star
process using Samtools - Support merging of multi-lane sequencing data into a single (pair) of
FASTQ files in the
upload-fastq-single
,upload-fastq-paired
,files-to-fastq-single
andfiles-to-fastq-paired
processes
24.0.0 - 2019-11-15¶
Added¶
- Add
resolwebio/slamdunk
Docker image - Add Tabix (1.7-2) to
resolwebio/bamliquidator:1.2.0
Docker image - Add
seqtk-rev-complement-single
andseqtk-rev-complement-paired
process - Add
slamdunk-all-paired
process
Changed¶
- BACKWARD INCOMPATIBLE: Require Resolwe 20.x
- Make BaseSpace file download more robust
- Bump
rose2
to 1.1.0,bamliquidator
to 1.3.8, and useresolwebio/base:ubuntu-18.04
Docker image as a base image inresolwebio/bamliquidator:1.1.0
Docker image - Use
resolwebio/bamliquidator:1.2.0
inrose2
process - Bump CPU, memory and Docker image (
resolwebio/rnaseq:4.9.0
) requirements inalignment-bwa-mem
,alignment-bwa-sw
andalignment-bwa-aln
processes - Use multi-threading option in Samtools commands in
alignment-bwa-mem
,alignment-bwa-sw
andalignment-bwa-aln
processes
23.1.1 - 2019-10-11¶
Changed¶
- Renamed
workflow-trim-align-quant
workflow to make the name more informative
23.1.0 - 2019-09-30¶
Added¶
- Add
Macaca mulatta
species choice to thesample
descriptor schema - Add
workflow-cutadapt-star-fc-quant-wo-depletion-single
process
Changed¶
- Test files improved for
workflow-wes
,bamclipper
,markduplicates
andbqsr
- Fix typo in
differentialexpression-shrna
process docstring
Fixed¶
- Fix transcript-to-gene_id mapping for Salmon expressions in
differentialexpression-deseq2
process. Transcript versions are now ignored when matching IDs using the transcript-to-gene_id mapping table. - Fix
workflow-cutadapt-star-fc-quant-single
process description
23.0.0 - 2019-09-17¶
Changed¶
- Update order of QC reports in MultiQC configuration file. The updated
configuration file is part of the
resolwebio/common:1.3.1
Docker image. - Bump Jbrowse to version 1.16.6 in
resolwebio/rnaseq:4.9.0
Docker image - Use JBrowse
generate-names.pl
script to index GTF/GFF3 features upon annotation file upload - Support Salmon reports in MultiQC and expose
dirs_depth
parameter - Expose transcript-level expression file in the
salmon-quant
process
Added¶
- Add
workflow-bbduk-salmon-qc-single
andworkflow-bbduk-salmon-qc-paired
workflows
Fixed¶
- Give process
upload-bedpe
access to network
22.0.0 - 2019-08-20¶
Changed¶
- BACKWARD INCOMPATIBLE: Require Resolwe 19.x
- BACKWARD INCOMPATIBLE: Unify
cutadapt-single
andcutadapt-paired
process inputs and refactor to use Cutadapt v2.4 - Expose BetaPrior parameter in
differentialexpression-deseq2
process - Install R from CRAN-maintained repositories in Docker images build
from the
resolwebio/base:ubuntu-18.04
base image - Prepare
resolwebio/common:1.3.0
Docker image:- Install R v3.6.1
- Bump Resdk to v10.1.0
- Install gawk package
- Fix Docker image build issues
- Use
resolwebio/common:1.3.0
as a base image forresolwebio/rnaseq:4.8.0
- Update StringTie to v2.0.0 in
resolwebio/rnaseq:4.8.0
- Support StringTie analysis results in DESeq2 tool
Added¶
- Add
cutadapt-3prime-single
process - Add
workflow-cutadapt-star-fc-quant-single
process - Add argument
skip
tobamclipper
which enables skipping of the said process - Add
cutadapt-corall-single
andcutadapt-corall-paired
processes for pre-processing of reads obtained using Corall Total RNA-seq library prep kit - Add
umi-tools-dedup
process - Add
stringtie
process - Add
workflow-corall-single
andworkflow-corall-paired
workflows optimized for Corall Total RNA-seq library prep kit data
Fixed¶
- Fix warning message in hierarchical clustering of genes. Incorrect gene names were reported in the warning message about removed genes. Computation of hierarchical clustering was correct.
21.0.1 - 2019-07-26¶
Changed¶
- Bump Cutadapt to v2.4 and use
resolwebio/common:1.2.0
as a base image inresolwebio/rnaseq:4.6.0
Added¶
- Add pigz package to
resolwebio/common:1.2.0
Docker image - Add StringTie and UMI-tools to
resolwebio/rnaseq:4.7.0
Docker image
Fixed¶
- Fix
spikeins-qc
process to correctly handle the case where all expressions are without spikeins - Fix an error in
macs2-callpeak
process that prevented correct reporting of build/species mismatch between inputs - Support UCSC annotations in
feature_counts
process by assigning empty string gene_ids to the “unknown” gene
21.0.0 - 2019-07-16¶
Changed¶
- BACKWARD INCOMPATIBLE: Require Resolwe 18.x
- Bump the number of allocated CPU cores to 20 in
alignment-bwa-mem
process - Bump memory requirements in
seqtk-sample-single
andseqtk-sample-paired
processes - Bump Salmon to v0.14.0 in
resolwebio/rnaseq:4.5.0
Docker image - Expose additional inputs in
salmon-index
process - Use
resolwebio/rnaseq:4.5.0
Docker image in processes that call Salmon tool (library-strandedness
,feature_counts
andqorts-qc
) - Implement dropdown menu for
upload-bedpe
process - Add validation stringency parameter to
bqsr
process and propagate it to theworkflow-wes
as well - Add LENIENT value to validation stringency parameter of the
markduplicates
process - Improve performance of RPKUM normalization in
featureCounts
process
Added¶
- Add
salmon-quant
process
Fixed¶
- Fix genome upload process to correctly handle filenames with dots
- Fix merging of expressions in
archive-samples
process. Previously some genes were missing in the merged expression files. The genes that were present had expression values correctly assigned. The process was optimized for performance and now supports parallelization.
20.0.0 2019-06-19¶
Changed¶
- BACKWARD INCOMPATIBLE: Require Resolwe 17.x
- BACKWARD INCOMPATIBLE: Use Elasticsearch version 6.x
- BACKWARD INCOMPATIBLE: Bump Django requirement to version 2.2
- BACKWARD INCOMPATIBLE: Remove obsolete RNA-seq workflows
workflow-bbduk-star-featurecounts-single
,workflow-bbduk-star-featurecounts-paired
,workflow-cutadapt-star-featurecounts-single
andworkflow-cutadapt-star-featurecounts-paired
- BACKWARD INCOMPATIBLE: Remove obsolete descriptor schemas:
rna-seq-bbduk-star-featurecounts
,quantseq
,rna-seq-cutadapt-star-featurecounts
andkapa-rna-seq-bbduk-star-featurecounts
- BACKWARD INCOMPATIBLE: In
upload-fasta-nucl
process, store compressed and uncompressed FASTA files infastagz
andfasta
ouput fields, respectively - Allow setting the Java memory usage flags for the QoRTs tool in
resolwebio/common:1.1.3
Docker image - Use
resolwebio/common:1.1.3
Docker image as a base image forresolwebio/rnaseq:4.4.2
- Bump GATK4 version to 4.1.2.0 in
resolwebio/dnaseq:4.2.0
- Use MultiQC configuration file and prepend directory name to sample
names by default in
multiqc
process - Bump
resolwebio/common
to 1.1.3 inresolwebio/dnaseq:4.2.0
- Process
vc-gatk4-hc
now also accepts BED files through parameterintervals_bed
Added¶
- Support Python 3.7
- Add Tabix (1.7-2) to
resolwebio/wgbs
docker image - Add JBrowse index output to
hmr
process - Add
bamclipper
tool andparallel
package toresolwebio/dnaseq:4.2.0
image - Support
hg19_mm10
hybrid genome inbam-split
process - Support mappability-based normalization (RPKUM) in featureCounts
- Add BEDPE upload process
- Add
bamclipper
process - Add
markduplicates
process - Add
bqsr
(BaseQualityScoreRecalibrator) process - Add whole exome sequencing (WES) pipeline
Fixed¶
- Fix building problems of
resolwebio/dnaseq
docker - Fix handling of no-adapters input in workflows
workflow-bbduk-star-featurecounts-qc-single
andworkflow-bbduk-star-featurecounts-qc-paired
19.0.1 2019-05-13¶
Fixed¶
- Use
resolwebio/rnaseq:4.4.2
Docker image that enforces the memory limit and bump memory requirements forqorts-qc
process - Bump memory requirements for
multiqc
process
19.0.0 2019-05-07¶
Changed¶
- Use Genialis fork of MultiQC 1.8.0b in
resolwebio/common:1.1.2
- Support Samtools idxstats and QoRTs QC reports in
multiqc
process - Support
samtools-idxstats
QC step in workflows:workflow-bbduk-star-featurecounts-qc-single
workflow-bbduk-star-featurecounts-qc-paired
workflow-bbduk-star-fc-quant-single
workflow-bbduk-star-fc-quant-paired
- Simplify
cellranger-count
outputs folder structure - Bump STAR aligner to version 2.7.0f in
resolwebio/rnaseq:4.4.1
Docker image - Use
resolwebio/rnaseq:4.4.1
inalignment-star
andalignment-star-index
processes - Save filtered count-matrix output file produced by DESeq2 differential expression process
Added¶
- Add
samtools-idxstats
process - Improve
cellranger-count
andcellranger-mkref
logging - Add FastQC report to
upload-sc-10x
process
Fixed¶
- Fix
archive-samples
to work withdata:chipseq:callpeak:macs2
data objects when downloading only peaks without QC reports - Fix parsing gene set files with empty lines to avoid saving gene sets with empty string elements
18.0.0 2019-04-16¶
Changed¶
- BACKWARD INCOMPATIBLE: Require Resolwe 16.x
- BACKWARD INCOMPATIBLE: Rename and improve descriptions of
processes specific to CATS RNA-seq kits. Remove related
cutadapt-star-htseq
descriptor schema. - BACKWARD INCOMPATIBLE: Remove
workflow-accel-gatk4
pipeline. Removeamplicon-panel
,amplicon-panel-advanced
andamplicon-master-file
descriptor schemas. - BACKWARD INCOMPATIBLE: Remove obsolete processes and descriptor
schemas:
rna-seq-quantseq
,bcm-workflow-rnaseq
,bcm-workflow-chipseq
,bcm-workflow-wgbs
,dicty-align-reads
,dicty-etc
,affy
andworkflow-chip-seq
- Expose additional parameters of
bowtie2
process - Support strandedness auto detection in
qorts-qc
process
Added¶
- Add shRNAde (v1.0) R package to the
resolwebio/rnaseq:4.4.0
Docker image - Add
resolwebio/scseq
Docker image - Add shRNA differential expression process. This is a two-step process which trims, aligns and quantifies short hairpin RNA species. These are then used in a differential expression.
- Add
sc-seq
processes:cellranger-mkref
cellranger-count
upload-sc-10x
upload-bam-scseq-indexed
Fixed¶
- Bump memory requirements in
seqtk-sample-single
andseqtk-sample-paired
processes - Fix
cellranger-count
html report - Mark spliced-alignments with XS flags in
workflow-rnaseq-cuffquant
- Fix whitespace handling in
cuffnorm
process
17.0.0 2019-03-19¶
Added¶
- Add
qorts-qc
(Quality of RNA-seq Tool-Set QC) process - Add
workflow-bbduk-star-fc-quant-single
andworkflow-bbduk-star-fc-quant-paired
processes - Add independent gene filtering and gene filtering based on Cook’s distance
in
DESeq2
differential expression process
Changed¶
- BACKWARD INCOMPATIBLE: Move gene filtering by expression count
input to
filter.min_count_sum
inDESeq2
differential expression process - BACKWARD INCOMPATIBLE: Require Resolwe 15.x
- Update
resolwebio/common:1.1.0
Docker image:- add QoRTs (1.3.0) package
- bump MultiQC to 1.7.0
- bump Subread package to 1.6.3
- Expose
maxns
input parameter inbbduk-single
andbbduk-paired
processes. Make this parameter available in workflowsworkflow-bbduk-star-featurecounts-qc-single
,workflow-bbduk-star-featurecounts-qc-paired
,workflow-bbduk-star-featurecounts-single
andworkflow-bbduk-star-featurecounts-paired
. - Save CPM-normalized expressions in
feature_counts
process. Control the default expression normalization type (exp_type
) using thenormalization_type
input. - Bump MultiQC to version 1.7.0 in
multiqc
process - Use
resolwebio/rnaseq:4.3.0
with Subread/featureCounts version 1.6.3 infeature_counts
process
16.3.0 2019-02-19¶
Changed¶
- Bump STAR aligner version to 2.7.0c in
resolwebio/rnaseq:4.2.2
- Processes
alignment-star
andalignment-star-index
now use Docker imageresolwebio/rnaseq:4.2.2
which contains STAR version2.7.0c
- Persistence of
basespace-file-import
process changed fromRAW
toTEMP
Added¶
- Make
prepare-geo-chipseq
work with bothdata:chipseq:callpeak:macs2
anddata:chipseq:callpeak:macs14
as inputs
Fixed¶
- Report correct total mapped reads and mapped reads percentage in
prepeak QC report for
data:alignment:bam:bowtie2
inputs inmacs2-callpeak
process
16.2.0 2019-01-28¶
Changed¶
- Enable multithreading mode in
alignment-bwa-aln
andalignment-bwa-sw
- Lineary lower the timeout for BigWig calculation when running on multiple cores
Fixed¶
- Remove
pip
--process-dependency-links
argument in testenv settings - Fix walt getting killed when
sort
runs out of memory. Thesort
command buffer size was limited to the process memory limit.
16.1.0 2019-01-17¶
Changed¶
Added¶
- Add the
FASTQ
file validator script to theupload-fastq-single
,upload-fastq-paired
,files-to-fastq-single
andfiles-to-fastq-paired
processes - Add
spikein-qc
process - Add to
resolwebio/rnaseq:4.1.0
Docker image:dnaio
Python library
- Add to
resolwebio/rnaseq:4.2.0
Docker image:- ERCC table
- common Genialis fonts and css file
- spike-in QC report template
- Set
MPLBACKEND
environment variable toAgg
inresolwebio/common:1.0.1
Docker image
Fixed¶
- Fix the format of the output
FASTQ
file in thedemultiplex.py
script - Fix NSC and RSC QC metric calculation for ATAC-seq and paired-end
ChIP-seq samples in
macs2-callpeak
andqc-prepeak
processes
16.0.0 2018-12-19¶
Changed¶
- BACKWARD INCOMPATIBLE: Require Resolwe 14.x
- BACKWARD INCOMPATIBLE: Remove obsolete processes
findsimilar
- BACKWARD INCOMPATIBLE: Include ENCODE-proposed QC analysis metrics
methodology in the
macs2-callpeak
process. Simplified MACS2 analysis inputs now allow the use of sample relations (treatment/background) concept to trigger multiple MACS2 jobs automatically using themacs2-batch
ormacs2-rose2-batch
processes. - BACKWARD INCOMPATIBLE: Update
workflow-atac-seq
inputs to match the updatedmacs2-callpeak
process - Use
resolwebio/rnaseq:4.0.0
Docker image inalignment-star-index
,bbduk-single
,bbduk-paired
,cuffdiff
,cufflinks
,cuffmerge
,cuffnorm
,cuffquant
,cutadapt-custom-single
,cutadapt-custom-paired
,cutadapt-single
,cutadapt-paired
,differentialexpression-deseq2
,differentialexpression-edger
,expression-aggregator
,feature_counts
,goenrichment
,htseq-count
,htseq-count-raw
,index-fasta-nucl
,library-strandedness
,pca
,regtools-junctions-annotate
,rsem
,salmon-index
,trimmomatic-single
,trimmomatic-paired
,upload-expression
,upload-expression-cuffnorm
,upload-expression-star
,upload-fasta-nucl
,upload-fastq-single
,upload-fastq-paired
,files-to-fastq-single
,files-to-fastq-paired
,upload-gaf
,upload-genome
,upload-gff3
,upload-gtf
andupload-obo
- Order statistical groups in expression aggregator output by sample descriptor field value
- Use
resolwebio/biox:1.0.0
Docker image inetc-bcm
,expression-dicty
andmappability-bcm
processes - Use
resolwebio/common:1.0.0
Docker image inamplicon-table
,mergeexpressions
,upload-diffexp
,upload-etc
,upload-multiplexed-single
andupload-multiplexed-paired
processes - Use
resolwebio/base:ubuntu-18.04
Docker image increate-geneset
,create-geneset-venn
,mergeetc
,prepare-geo-chipseq
,prepare-geo-rnaseq
,upload-cxb
,upload-geneset
,upload-header-sam
,upload-mappability
,upload-snpeff
andupload-picard-pcrmetrics
processes - Update GATK4 to version 4.0.11.0 in
resolwebio/dnaseq:4.1.0
Docker image. Install and use JDK v8 by default to ensure compatibility with GATK4 package. - Use
resolwebio/dnaseq:4.1.0
Docker image inalign-bwa-trim
,coveragebed
,filtering-chemut
,lofreq
,picard-pcrmetrics
,upload-master-file
,upload-variants-vcf
andvc-gatk4-hc
processes - Expose reads quality filtering (q) parameter, reorganize inputs and
rename the stats output file in
alignment-bwa-aln
process - Use
resolwebio/chipseq:4.0.0
Docker image inchipseq-genescore
,chipseq-peakscore
,macs14
,upload-bed
andqc-prepeak
processes - Use
resolwebio/bamliquidator:1.0.0
Docker image inbamliquidator
andbamplot
processes
Added¶
- Add biosample source field to
sample
descriptor schema - Add
background_pairs
Jinja expressions filter that accepts a list of data objects and orders them in a list of pairs (case, background) based on the background relation between corresponding samples - Add
chipseq-bwa
descriptor schema. This schema specifies the default inputs for BWA ALN aligner process as defined in ENCODE ChIP-Seq experiments. - Add support for MACS2 result files to MultiQC process
- Add
macs2-batch
,macs2-rose2-batch
andworkflow-macs-rose
processes - Add feature symbols to expressions in
archive-samples
process
Fixed¶
- Make ChIP-seq fields in
sample
descriptor schema visible when ChIPmentation assay type is selected - Fix handling of whitespace in input BAM file name in script
detect_strandedness.sh
- Set available memory for STAR aligner to 36GB. Limit the available
memory for STAR aligner
--limitBAMsortRAM
parameter to 90% of the Docker requirements setting - Set
bbduk-single
andbbduk-paired
memory requirements to 8GB - Fix wrong file path in
archive-samples
process
15.0.0 2018-11-20¶
Changed¶
- BACKWARD INCOMPATIBLE: Remove obsolete processes:
bsmap
,mcall
,coverage-garvan
,igv
,jbrowse-bed
,jbrowse-gff3
,jbrowse-gtf
,jbrowse-bam-coverage
,jbrowse-bam-coverage-normalized
,jbrowse-refseq
,fastq-mcf-single
,fastq-mcf-paired
,hsqutils-trim
,prinseq-lite-single
,prinseq-lite-paired
,sortmerna-single
,sortmerna-paired
,bam-coverage
,hsqutils-dedup
,vc-samtools
,workflow-heat-seq
andalignment-tophat2
- BACKWARD INCOMPATIBLE: Remove
jbrowse-bam-coverage
process step from theworkflow-accel
workflow. The bigwig coverage track is computed inalign-bwa-trim
process instead. - BACKWARD INCOMPATIBLE: Remove
resolwebio/utils
Docker image. This image is replaced by theresolwebio/common
image. - BACKWARD INCOMPATIBLE: Use
resolwebio/common
Docker image as a base image for theresolwebio/biox
,resolwebio/chipseq
,resolwebio/dnaseq
andresolwebio/rnaseq
images - BACKWARD INCOMPATIBLE: Remove
resolwebio/legacy
Docker image. - Use sample name as the name of the data object in:
alignment-bwa-aln
alignment-bowtie2
qc-prepeak
macs2-callpeak
- Attach
macs2-callpeak
,macs14
androse2
process data to the case/treatment sample - Use
resolwebio/dnaseq:4.0.0
docker image inalign-bwa-trim
process - Use
resolwebio/rnaseq:4.0.0
docker image in aligners:alignment-bowtie
,alignment-bowtie2
,alignment-bwa-mem
,alignment-bwa-sw
,alignment-bwa-aln
,alignment-hisat2
,alignment-star
andalignment-subread
. - Set memory limits in
upload-genome
,trimmomatic-single
andtrimmomatic-paired
processes - Improve error messages in differential expression process
DESeq2
Added¶
- Add
makedb (WALT 1.01)
- callable asmakedb-walt
, tool to create genome index for WALT aligner, toresolwebio/rnaseq
docker image - Add
resolwebio/wgbs
docker image including the following tools:MethPipe (3.4.3)
WALT (1.01)
wigToBigWig (kent-v365)
- Add
resolwebio/common
Docker image. This image includes common bioinformatics utilities and can serve as a base image for other, specializedresolwebio
Docker images:resolwebio/biox
,resolwebio/chipseq
,resolwebio/dnaseq
andresolwebio/rnaseq
. - Add
shift
(user-defined cross-correlation peak strandshift) input toqc-prepeak
process - Add ATAC-seq workflow
- Compute index for
WALT
aligner on genome upload and support uploading the index together with the genome - Add
Whole genome bisulfite sequencing
workflow and related WGBS processes:WALT
methcounts
HMR
- Add bedClip to resolwebio/chipseq:3.1.0 docker image
- Add
resolwebio/biox
Docker image. This image is based on theresolwebio/common
image and includes Biox Python library for Dictyostelium RNA-Seq analysis support. - Add
resolwebio/snpeff
Docker image. The image includes SnpEff (4.3K) tool. - Add spike-in names, rRNA and globin RNA cromosome names in
resolwebio/common
image - Add UCSC bedGraphtoBigWig tool for calculating BigWig in
bamtobigwig.sh
script. Inalign-bwa-trim
processor set this option (that BigWig is calculated by UCSC tool instead of deepTools), because it is much faster for amplicon files. In other processors update the input parameters forbamtobigwig.sh
:alignment-bowtie
,alignment-bowtie2
,alignment-bwa-mem
,alignment-bwa-sw
,alignment-bwa-aln
,alignment-hisat2
,alignment-star
alignment-subread
,upload-bam
,upload-bam-indexed
andupload-bam-secondary
. - In
bamtobigwig.sh
don’t create BigWig when bam file was aligned on globin RNA or rRNA (this are QC steps and BigWig is not needed)
Fixed¶
- BACKWARD INCOMPATIBLE: Use user-specificed distance metric in hierarchical clustering
- Handle integer expression values in hierarchical clustering
- Fix Amplicon table gene hyperlinks for cases where multiple genes are associated with detected variant
- Handle empty gene name in expression files in PCA
- Fix PBC QC reporting in
qc-prepeak
process for a case where there are no duplicates in the input bam - Fix
macs2-callpeak
process so that user defined fragment lenth has priority over theqc-prepeak
estimated fragment length when shifting reads for post-peakcall QC - Fix
macs2-callpeak
to prevent the extension of intervals beyond chromosome boundaries in MACS2 bedgraph outputs - Fix warning message in hierarchical clustering of genes to display gene names
14.0.2 2018-10-23¶
Fixed¶
- Fix
htseq-count-raw
process to correctly map features with associated feature symbols.
14.0.1 2018-10-23¶
Fixed¶
- Handle missing gene expression in hierarchical clustering of genes. If one or more genes requested in gene filter are missing in selected expression files a warning is issued and hierarchical clustering of genes is computed with the rest of the genes instead of failing.
- Fix PCA computation for single sample case
14.0.0 2018-10-09¶
Changed¶
- BACKWARD INCOMPATIBLE: Require Resolwe 13.x
- BACKWARD INCOMPATIBLE: Remove
gsize
input frommacs2-callpeak
process and automate genome size selection - BACKWARD INCOMPATIBLE: Set a new default
sample
andreads
descriptor schema. Change slug fromsample2
tosample
, modify group names, addcell_type
field to the newsample
descriptor schema, and remove the originalsample
,sample-detailed
, andreads-detailed
descriptor schemas. - BACKWARD INCOMPATIBLE: Unify types of
macs14
andmacs2-callpeak
processes and makerose2
work with both - BACKWARD INCOMPATIBLE: Remove
replicates
input incuffnorm
process. Use sample relation information instead. - Use
resolwebio/chipseq:3.0.0
docker image in the following processes:macs14
macs2-callpeak
rose2
- Downgrade primerclip to old version (v171018) in
resolwebio/dnaseq:3.3.0
docker image and move it to google drive. - Move
bam-split
process toresolwebio/rnaseq:3.7.1
docker image - Count unique and multimmaping reads in
regtools-junctions-annotate
process
Added¶
- Add
qc-prepeak
process that reports ENCODE3 accepted ChIP-seq and ATAC-seq QC metrics - Add QC report to
macs2-callpeak
process - Add combining ChIP-seq QC reports in
archive-samples
process - Add detection of globin-derived reads as an additional QC step in the
workflow-bbduk-star-featurecounts-qc-single
andworkflow-bbduk-star-featurecounts-qc-paired
processes. - Add mappings from ENSEMBL or NCBI to UCSC chromosome names and deepTools
(v3.1.0) to
resolwebio/dnaseq:3.3.0
docker image - Add BigWig output field to following processors:
align-bwa-trim
upload-bam
upload-bam-indexed
upload-bam-secondary
- Add
replicate_groups
Jinja expressions filter that accepts a list of data objects and returns a list of labels determining replicate groups. - Add ‘Novel splice junctions in BED format’ output to
regtools-junctions-annotate
process, so that user can visualize only novel splice juntions in genome browsers.
Fixed¶
- Fix handling of numerical feature_ids (NCBI source) in
create_expression_set.py
script - Make
chipseq-peakscore
work with gzipped narrowPeak input frommacs2-callpeak
- Use uncompressed FASTQ files as input to STAR aligner to prevent issues on (network) filesystems without FIFO support
13.0.0 2018-09-18¶
Changed¶
- BACKWARD INCOMPATIBLE: Require Resolwe 12.x
- BACKWARD INCOMPATIBLE: Remove obsolete processes:
assembler-abyss
,cutadapt-amplicon
,feature_location
,microarray-affy-qc
,reads-merge
,reference_compatibility
,transmart-expressions
,upload-hmmer-db
,upload-mappability-bigwig
,upload-microarray-affy
. - BACKWARD INCOMPATIBLE: Remove obsolete descriptor schema:
transmart
. - BACKWARD INCOMPATIBLE: Remove tools which are not used by any process:
clustering_leaf_ordering.py
,go_genesets.py
,VCF_ad_extract.py
,volcanoplot.py
,xgff.py
,xgtf2gff.py
. - BACKWARD INCOMPATIBLE: Management command for inserting features and mappings requires PostgreSQL version 9.5 or newer
- Update the meta data like name, description, category, etc. of most of the processes
- Speed-up management command for inserting mappings
- Change location of cufflinks to Google Drive for resolwebio/rnaseq Docker build
- Calculate alignment statistics for the uploaded alignment (.bam) file in the
upload-bam
,upload-bam-indexed
andupload-bam-secondary
processes. - Annotation (GTF/GFF3) file input is now optional for the creation of the STAR genome index files. Annotation file can be used at the alignment stage to supplement the genome indices with the set of known features.
- Trigger process warning instead of process error in the case when
bamtobigwig.sh
scripts detects an empty .bam file. - Set the default reads length filtering parameter to 30 bp in the
rna-seq-bbduk-star-featurecounts
andkapa-rna-seq-bbduk-star-featurecounts
experiment descriptor schema. Expand the kit selection choice options in the latter descriptor schema.
Added¶
- Add
MultiQC (1.6.0)
andSeqtk (1.2-r94)
to theresolwebio/utils:1.5.0
Docker image - Add
sample2
descriptor schema which is the successor of the originalsample
andreads
descriptor schemas - Add bedToBigBed and Tabix to resolwebio/rnaseq:3.7.0 docker image
- Add
HS Panel
choice option to theamplicon-master-file
descriptor schema - Add MultiQC process
- Add process for the Seqtk tool
sample
sub-command. This process allows sub-sampling of.fastq
files using either a fixed number of reads or the ratio of the input file. - Add MultiQC analysis step to the
workflow-bbduk-star-featurecounts-single
andworkflow-bbduk-star-featurecounts-single
processes. - Add
workflow-bbduk-star-featurecounts-qc-single
andworkflow-bbduk-star-featurecounts-qc-paired
processes which support MultiQC analysis, input reads down-sampling (using Seqtk) and rRNA sequence detection using STAR aligner. - Add to
resolwebio/chipseq
Docker image:bedtools (2.25.0-1)
gawk (1:4.1.3+dfsg-0.1)
picard-tools (1.113-2)
run_spp.R (1.2) (as spp)
SPP (1.14)
- Add
regtools-junctions-annotate
process that annotates novel splice junctions. - Add
background
relation type to fixtures
Fixed¶
- Track
source
information in theupload-fasta-nucl
process. - When STAR aligner produces an empty alignment file, re-sort the alignment
file to allow successful indexing of the output
.bam
file. - Create a symbolic link to the alignment file in the
feature_counts
process, so that relative path is used in the quantification results. This prevent the FeatureCounts output to be listed as a separate sample in the MultiQC reports. - Fix handling of expression objects in
archive-samples
process
12.0.0 - 2018-08-13¶
Changed¶
- BACKWARD INCOMPATIBLE: Require Resolwe 11.x
- BACKWARD INCOMPATIBLE: Use read count instead of sampling rate in strandedness detection
- BACKWARD INCOMPATIBLE: Remove
genome
input fromrose2
process and automate its selection - BACKWARD INCOMPATIBLE: Refactor
cutadapt-paired
process - BACKWARD INCOMPATIBLE: Improve leaf ordering performance in gene and
sample hierarchical clustering. We now use exact leaf ordering which has
been recently added to
scipy
instead of an approximate in-house solution based on nearest neighbor algorithm. Add informative warning and error messages to simplify troubleshooting with degenerate datasets. - Remove
igvtools
fromresolwebio/utils
Docker image - Improve helper text and labels in processes used for sequencing data upload
- Allow using custom adapter sequences in the
workflow-bbduk-star-featurecounts-single
andworkflow-bbduk-star-featurecounts-paired
processes - Change chromosome names from ENSEMBL / NCBI to UCSC (example: “1” to “chr1”) in BigWig files. The purpose of this is to enable viewing BigWig files in UCSC genome browsers for files aligned with ENSEBML or NCBI genome. This change is done by adding script bigwig_chroms_to_ucsc.py to bamtobigwig.sh script.
- Reduce RAM requirement in SRA import processes
Added¶
- Add two-pass mode to
alignment-star
process - Add
regtools (0.5.0)
toresolwebio/rnaseq
Docker image - Add KAPA experiment descriptor schema
- Add
resdk
Python 3 package toresolwebio/utils
Docker image - Add to
cutadapt-single
process an option to discard reads having more ‘N’ bases than specified. - Add workflows for single-end
workflow-cutadapt-star-featurecounts-single
and paired-end readsworkflow-cutadapt-star-featurecounts-paired
. Both workflows consist of preprocessing with Cutadapt, alignment with STAR two pass mode and quantification with featureCounts. - Add descriptor schema
rna-seq-cutadapt-star-featurecounts
Fixed¶
- BACKWARD INCOMPATIBLE: Fix the
stitch
parameter handling inrose2
- fix
upload-gtf
to create JBrowse track only if GTF file is ok - Pin
sra-toolkit
version to 2.9.0 inresolwebio/utils
Docker image. - Fix and improve
rose2
error messages - Fail gracefully if bam file is empty when producing bigwig files
- Fail gracefully if there are no matches when mapping chromosome names
11.0.0 - 2018-07-17¶
Changed¶
- BACKWARD INCOMPATIBLE: Remove management command module
- BACKWARD INCOMPATIBLE: Remove filtering of genes with low expression in PCA analysis
- BACKWARD INCOMPATIBLE: Remove obsolete RNA-seq DSS process
- Expand error messages in
rose2
process - Check for errors during download of FASTQ files and use
resolwebio/utils:1.3.0
Docker image in import SRA process - Increase Feature’s full name’s max length to 350 to support a long full name of “Complement C3 Complement C3 beta chain C3-beta-c Complement C3 alpha chain C3a anaphylatoxin Acylation stimulating protein Complement C3b alpha’ chain Complement C3c alpha’ chain fragment 1 Complement C3dg fragment Complement C3g fragment Complement C3d fragment Complement C3f fragment Complement C3c alpha’ chain fragment 2” in Ensembl
Added¶
- Add exp_set and exp_set_json output fields to expression processes:
feature_counts
htseq-count
htseq-count-raw
rsem
upload-expression
upload-expression-cuffnorm
upload-expression-star
- Add ‘Masking BED file’ input to
rose2
process which allows masking reagions from the analysis - Add
filtering.outFilterMismatchNoverReadLmax
input toalignment-star
process - Add mappings from ENSEMBL or NCBI to UCSC chromosome names to
resolwebio/rnaseq:3.5.0
docker image
Fixed¶
- Fix peaks BigBed output in
macs14
process - Remove duplicated forward of
alignIntronMax
input field in BBDuk - STAR - featureCounts workflow - Make
cuffnorm
process attach correct expression data objects to samples - Fix
upload-gtf
in a way that GTF can be shown in JBrowse. Because JBrowse works only with GFF files, input GTF is converted to GFF from which JBrowse track is created.
10.0.1 - 2018-07-06¶
Fixed¶
- Fix
bamtobigwig.sh
to timeout thebamCoverage
calculation after defined time
10.0.0 - 2018-06-19¶
Added¶
- Add to
resolwebio/chipseq
Docker image:Bedops (v2.4.32)
Tabix (v1.8)
python3-pandas
bedGraphToBigWig (kent-v365)
bedToBigBed (kent-v365)
- Add to
resolwebio/rnaseq:3.2.0
Docker image:genometools (1.5.9)
igvtools (v2.3.98)
jbrowse (v1.12.0)
Bowtie (v1.2.2)
Bowtie2 (v2.3.4.1)
BWA (0.7.17-r1188)
TopHat (v2.1.1)
Picard Tools (v2.18.5)
bedGraphToBigWig (kent-v365)
- Add Debian package
file
toresolwebio/rnaseq:3.3.0
Docker image - Support filtering by type on feature API endpoint
- Add BigWig output field to following processes:
alignment-bowtie
alignment-bowtie2
alignment-tophat2
alignment-bwa-mem
alignment-bwa-sw
alignment-bwa-aln
alignment-hisat2
alignment-star
- Add Jbrowse track output field to
upload-genome
processor. - Use
reslowebio/rnaseq
Docker image and add Jbrowse track and IGV sorting and indexing to following processes:upload-gff3
upload-gtf
gff-to-gtf
- Add Tabix index for Jbrowse to
upload-bed
processor and usereslowebio/rnaseq
Docker image - Add BigWig, BigBed and JBrowse track outputs to
macs14
process - Add Species and Build outputs to
rose2
process - Add Species, Build, BigWig, BigBed and JBrowse track outputs to
macs2
process - Add
scipy
(v1.1.0) Python 3 package toresolwebio/utils
Docker image
Changed¶
BACKWARD INCOMPATIBLE: Drop support for Python 3.4 and 3.5
BACKWARD INCOMPATIBLE: Require Resolwe 10.x
BACKWARD INCOMPATIBLE: Upgrade to Django Channels 2
BACKWARD INCOMPATIBLE: Count fragments (or templates) instead of reads by default in
featureCounts
process andBBDuk - STAR - featureCounts
pipeline. The change applies only to paired-end data.BACKWARD INCOMPATIBLE: Use
resolwebio/rnaseq:3.2.0
Docker image in the following processes that output reads:upload-fastq-single
upload-fastq-paired
files-to-fastq-single
files-to-fastq-paired
reads-merge
bbduk-single
bbduk-paired
cutadapt-single
cutadapt-paired
cutadapt-custom-single
cutadapt-custom-paired
trimmomatic-single
trimmomatic-paired
.
This change unifies the version of
FastQC
tool (0.11.7) used for quality control of reads in the aforementioned processes. The new Docker image comes with an updated version of Cutadapt (1.16) which affects the following processes:cutadapt-single
cutadapt-paired
cutadapt-custom-single
cutadapt-custom-paired
.
The new Docker image includes also an updated version of Trimmomatic (0.36) used in the following processes:
upload-fastq-single
upload-fastq-paired
files-to-fastq-single
files-to-fastq-paired
trimmomatic-single
trimmomatic-paired
.
BACKWARD INCOMPATIBLE: Change Docker image in
alignment-subread
fromresolwebio/legacy:1.0.0
with Subread (v1.5.1) toresolwebio/rnaseq:3.2.0
with Subread (v1.6.0).--multiMapping
option was added instead of--unique_reads
. By default aligner report uniquely mapped reads only.Update
wigToBigWig
to kent-v365 version inresolwebio/chipseq
Docker imageChange paths in HTML amplicon report template in
resolwebio/dnaseq
Docker imageMove assay type input in BBDuk - STAR - featureCounts pipeline descriptor schema to advanced options
Use
resolwebio/rnaseq:3.2.0
Docker image with updated versions of tools instead ofresolwebio/legacy:1.0.0
Docker image in following processes:alignment-bowtie
with Bowtie (v1.2.2) instead of Bowtie (v1.1.2)alignment-bowtie2
with Bowtie2 (v2.3.4.1) instead of Bowtie2 (v2.2.6)alignment-tophat2
with TopHat (v2.1.1) instead of TopHat (v2.1.0)alignment-bwa-mem
,alignment-bwa-sw` and ``alignment-bwa-aln
with BWA (v0.7.17-r1188) instead of BWA (v0.7.12-r1039)alignment-hisat2
with HISAT2 (v2.1.0) instead of HISAT2 (v2.0.3-beta)upload-genome
Use
resolwebio/base:ubuntu-18.04
Docker image as a base image inresolwebio/utils
Docker imageUpdate Python 3 packages in
resolwebio/utils
Docker image:numpy
(v1.14.4)pandas
(v0.23.0)
Replace
bedgraphtobigwig
withdeepTools
inresolwebio/rnaseq
Docker image, due to faster performanceUse
resolwebio/rnaseq:3.3.0
Docker image inalignment-star-index
with STAR (v2.5.4b)
Fixed¶
- Make management commands use a private random generator instance
- Fix output
covplot_html
ofcoveragebed
process - Fix process
archive-samples
andamplicon-archive-multi-report
to correctly handle nested file paths - Change
rose2
andchipseq-peakscore
to work with.bed
or.bed.gz
input files - Fix the
expression-aggregator
process so that it tracks thespecies
of the input expression data - Fix
bamtobigwig.sh
to usedeepTools
instead ofbedtools
withbedgraphToBigWig
due to better time performance
9.0.0 - 2018-05-15¶
Changed¶
- BACKWARD INCOMPATIBLE: Simplify the
amplicon-report
process inputs by using Latex report template from theresolwebio/latex
Docker image assets - BACKWARD INCOMPATIBLE: Simplify the
coveragebed
process inputs by using Bokeh assets from theresolwebio/dnaseq
Docker image - BACKWARD INCOMPATIBLE: Require Resolwe 9.x
- Update
wigToBigWig
tool inresolwebio/chipseq
Docker image - Use
resolwebio/rnaseq:3.1.0
Docker image in the following processes:cufflinks
cuffnorm
cuffquant
- Remove
differentialexpression-limma
process - Use
resolwebio/rnaseq:3.1.0
docker image and expand error messages in:cuffdiff
differentialexpression-deseq2
differentialexpression-edger
- Update
workflow-bbduk-star-htseq
- Update
quantseq
descriptor schema - Assert species and build in
htseq-count-normalized
process - Set amplicon report template in
resolwebio/latex
Docker image to landscape mode
Added¶
- Support Python 3.6
- Add
template_amplicon_report.tex
toresolwebio/latex
Docker image assets - Add SnpEff tool and bokeh assets to
resolwebio/dnaseq
Docker image - Add automated library strand detection to
feature_counts
quantification process - Add FastQC option
nogroup
tobbduk-single
andbbduk-paired
processes - Add CPM normalization to
htseq-count-raw
process - Add
workflow-bbduk-star-htseq-paired
- Add legend to amplicon report template in
resolwebio/latex
Docker image
Fixed¶
- Fix manual installation of packages in Docker images to handle dots and spaces in file names correctly
- Fix COSMIC url template in
amplicon-table
process - Fix Create IGV session in Archive samples process
- Fix
source
tracking incufflinks
andcuffquant
processes - Fix amplicon master file validation script. Check and report error if duplicated amplicon names are included. Validation will now pass also for primer sequences in lowercase.
- Fix allele frequency (AF) calculation in
snpeff
process - Fix bug in script for calculating FPKM. Because genes of raw counts from
featureCounts
were not lexicographically sorted, division of normalized counts was done with values from other, incorrect, genes. Results fromfeatureCounts
, but notHTSeq-count
process, were affected.
8.1.0 - 2018-04-13¶
Changed¶
- Use the latest versions of the following Python packages in
resolwebio/rnaseq
docker image: Cutadapt 1.16, Apache Arrow 0.9.0, pysam 0.14.1, requests 2.18.4, appdirs 1.4.3, wrapt 1.10.11, PyYAML 3.12 - Bump tools version in
resolwebio/rnaseq
docker image:- Salmon to 0.9.1
- FastQC to 0.11.7
- Generalize the no-extraction-needed use-case in
resolwebio/base
Docker imagedownload_and_verify
script
Added¶
- Add the following Python packages to
resolwebio/rnaseq
docker image: six 1.11.0, chardet 3.0.4, urllib3 1.22, idna 2.6, and certifi 2018.1.18 - Add
edgeR
R library toresolwebio/rnaseq
docker image - Add Bedtools to
resolwebio/rnaseq
docker image
Fixed¶
- Handle filenames with spaces in the following processes:
alignment-star-index
alignment-tophat2
cuffmerge
index-fasta-nucl
upload-fasta-nucl
- Fix COSMIC url template in (multisample) amplicon reports
8.0.0 - 2018-04-11¶
Changed¶
- BACKWARD INCOMPATIBLE: Refactor
trimmomatic-single
,trimmomatic-paired
,bbduk-single
, andbbduk-paired
processes - BACKWARD INCOMPATIBLE: Merge
align-bwa-trim
andalign-bwa-trim2
process functionality. Retain only the refactored process under slugalign-bwa-trim
- BACKWARD INCOMPATIBLE: In processes handling VCF files, the output
VCF files are stored in bgzip-compressed form. Tabix index is not referenced
to an original VCF file anymore, but stored in a separate
tbi
output field - BACKWARD INCOMPATIBLE: Remove an obsolete
workflow-accel-2
workflow - BACKWARD INCOMPATIBLE: Use Elasticsearch version 5.x
- BACKWARD INCOMPATIBLE: Parallelize execution of the following processes:
alignment-bowtie2
alignment-bwa-mem
alignment-hisat2
alignment-star
alignment-tophat2
cuffdiff
cufflinks
cuffquant
- Require Resolwe 8.x
- Bump STAR aligner version in
resolwebio/rnaseq
docker image to 2.5.4b - Bump Primerclip version in
resolwebio/dnaseq
docker image - Use
resolwebio/dnaseq
Docker image inpicard-pcrmetrics
process - Run
vc-realign-recalibrate
process using multiple cpu cores to optimize the processing time - Use
resolwebio/rnaseq
Docker image inalignment-star
process
Added¶
- Add CNVKit, LoFreq and GATK to
resolwebio/dnaseq
docker image - Add BaseSpace files download tool
- Add process to import a file from BaseSpace
- Add process to convert files to single-end reads
- Add process to convert files to paired-end reads
- Add
vc-gatk4-hc
process which implements GATK4 HaplotypeCaller variant calling tool - Add
workflow-accel-gatk4
pipeline that uses GATK4 HaplotypeCaller as an alternative to GATK3 used inworkflow-accel
pipeline - Add
amplicon-master-file
descriptor schema - Add
workflow-bbduk-star-featurecounts
pipeline - Add
rna-seq-bbduk-star-featurecounts
RNA-seq descriptor schema
Fixed¶
- Fix iterative trimming in
bowtie
andbowtie2
processes - Fix
archive-samples
to use sample names for headers when merging expressions - Improve
goea.py
tool to handle duplicated mapping results - Handle filenames with spaces in the following processes:
alignment-hisat2
alignment-bowtie
prepare-geo-chipseq
prepare-geo-rnaseq
cufflinks
cuffquant
7.0.1 - 2018-03-27¶
Fixed¶
- Use name-ordered BAM file for counting reads in
HTSeq-count
process by default to avoid buffer overflow with large BAM files
7.0.0 - 2018-03-13¶
Changed¶
- BACKWARD INCOMPATIBLE: Remove Ubuntu 17.04 base Docker image since it has has reached its end of life and change all images to use the new ubuntu 17.10 base image
- BACKWARD INCOMPATIBLE: Require
species
andbuild
inputs in the following processes:upload-genome
upload-gtf
upload-gff3
upload-bam
upload-bam-indexed
- BACKWARD INCOMPATIBLE: Track
species
andbuild
information in the following processes:cuffmerge
- alignment processes
- variant calling processes
- JBrowse processes
- BACKWARD INCOMPATIBLE: Track
species
,build
andfeature_type
in the following processes:upload-expression-star
- quantification processes
- differential expression processes
- BACKWARD INCOMPATIBLE: Track
species
in gene set (Venn) andgoenrichment
processes - BACKWARD INCOMPATIBLE: Rename
genes_source
input tosource
in hierarchical clustering and PCA processes - BACKWARD INCOMPATIBLE: Remove the following obsolete processes:
- Dictyostelium-specific ncRNA quantification
go-geneset
- bayseq differential expression
cuffmerge-gtf-to-gff3
transdecoder
web-gtf-dictybase
upload-rmsk
snpdat
- BACKWARD INCOMPATIBLE: Unify output fields of processes of type
data:annotation
- BACKWARD INCOMPATIBLE: Rename the organism field names to species in
rna-seq
andcutadapt-star-htseq
descriptor schemas - BACKWARD INCOMPATIBLE: Rename the
genome_and_annotation
field name tospecies
inbcm-*
descriptor schemas and use the full species name for thespecies
field values - BACKWARD INCOMPATIBLE: Refactor
featureCounts
process - BACKWARD INCOMPATIBLE: Change
import-sra
process to work withresolwebio/utils
Docker image and refactor its inputs - Require Resolwe 7.x
- Add environment export for Jenkins so that the manager will use a globally-unique channel name
- Set
scheduling_class
of gene and sample hierarchical clustering processes tointeractive
- Change base Docker images of
resolwebio/rnaseq
andresolwebio/dnaseq
toresolwebio/base:ubuntu-18.04
- Use the latest versions of the following Python packages in
resolwebio/rnaseq
Docker image: Cutadapt 1.15, Apache Arrow 0.8.0, pysam 0.13, and xopen 0.3.2 - Use the latest versions of the following Python packages in
resolwebio/dnaseq
Docker image: Bokeh 0.12.13, pandas 0.22.0, Matplotlib 2.1.2, six 1.11.0, PyYAML 3.12, Jinja2 2.10, NumPy 1.14.0, Tornado 4.5.3, and pytz 2017.3 - Use the latest version of
wigToBigWig
tool inresolwebio/chipseq
Docker image - Use
resolwebio/rnaseq:3.0.0
Docker image ingoenrichment
,upload-gaf
andupload-obo
processes - Use
resolwebio/dnaseq:3.0.0
Docker image infiltering_chemut
process - Change
cuffnorm
process type todata:cuffnorm
- Set type of
coverage-garvan
process todata:exomecoverage
- Remove
gsize
input frommacs14
process and automate genome size selection - Adjust
bam-split
process so it can be included in workflows - Make ID attribute labels in
featureCounts
more informative - Change ‘source’ to ‘gene ID database’ in labes and descriptions
- Change
archive-samples
process to create different IGV session files forbuild
andspecies
- Expose advanced parameters in Chemical Mutagenesis workflow
- Clarify some descriptions in the
filtering_chemut
process andchemut
workflow - Change expected genome build formatting for hybrid genomes in
bam-split
process - Set the
cooksCutoff
parameter toFALSE
indeseq.R
tool - Rename ‘Expressions (BCM)’ to ‘Dicty expressions’
Added¶
- Mechanism to override the manager’s control channel prefix from the environment
- Add Ubuntu 17.10 and Ubuntu 18.04 base Docker images
- Add
resolwebio/utils
Docker image - Add
BBMap
,Trimmomatic
,Subread
,Salmon
, anddexseq_prepare_annotation2
tools andDEXSeq
andloadSubread
R libraries toresolwebio/rnaseq
Docker image - Add abstract processes that ensure that all processes that inherit from them
have the input and output fields that are defined in them:
abstract-alignment
abstract-annotation
abstract-expression
abstract-differentialexpression
abstract-bed
- Add miRNA workflow
- Add
prepare-geo-chipseq
andprepare-geo-rnaseq
processes that produce a tarball with necessary data and folder structure for GEO upload - Add
library-strandedness
process which uses theSalmon
tool built-in functionality to detect the library strandedness information - Add
species
andgenome build
output fields tomacs14
process - Expose additional parameters in
alignment-star
,cutadapt-single
andcutadapt-paired
processes - Add
merge expressions
toarchive-samples
process - Add description of batch mode to Expression aggregator process
- Add error and warning messages to the
cuffnorm
process - Add optional
species
input to hierarchical clustering and PCA processes - Add Rattus norvegicus species choice to the
rna-seq
descriptor schema to allow running RNA-seq workflow for this species from the Recipes
Fixed¶
- Fix custom argument passing script for
Trimmomatic
inresolwebio/rnaseq
Docker image - Fix installation errors for
dexseq-prepare-annotation2
inresolwebio/rnaseq
Docker image - Fix
consensus_subreads
input option in Subread process - Limit variant-calling process in the chemical mutagenesis workflow and the Picard tools run inside to 16 GB of memory to prevent them from crashing because they try to use too much memory
- The chemical mutagenesis workflow was erroneously categorized as
data:workflow:rnaseq:cuffquant
type. This is switched todata:workflow:chemut
type. - Fix handling of NA values in Differential expression results table. NA values were incorrectly replaced with value 0 instead of 1
- Fix
cuffnorm
process to work with samples containing dashes in their name and dispense prefixing sample names starting with numbers with ‘X’ in thecuffnorm
normalization outputs - Fix
cuffnorm
process’ outputs to correctly track species and build information - Fix typos and sync parameter description common to
featureCounts
andmiRNA
workflow
6.2.2 - 2018-02-21¶
Fixed¶
- Fix
cuffnorm
process to correctly use sample names as labels in output files and expandcuffnorm
tests
6.2.1 - 2018-01-28¶
Changed¶
- Update description text of
cutadapt-star-htseq
descriptor schema to better describe the difference between gene/transcript-type analyses - Speed-up management command for inserting mappings
6.2.0 - 2018-01-17¶
Added¶
- Add R, tabix, and CheMut R library to
resolwebio/dnaseq
Docker image - Add
SRA Toolkit
toresolwebio/rnaseq
Docker image
Changed¶
- Require Resolwe 6.x
- Extend pathway map with species and source field
- Move template and logo for multi-sample report into
resolwebio/latex
Docker image - Refactor
amplicon-report
process to contain all relevant inputs foramplicon-archive-multi-report
- Refactor
amplicon-archive-multi-report
- Use
resolwebio/dnaseq:1.2.0
Docker image infiltering_chemut
process
Fixed¶
- Enable DEBUG setting in tests using Django’s
LiveServerTestCase
- Wait for ElasticSeach to index the data in
KBBioProcessTestCase
- Remove unused parameters in TopHat (2.0.13) process and Chip-seq workflow
6.1.0 - 2017-12-12¶
Added¶
- Add
amplicon-archive-multi-report
process - Add
upload-metabolic-pathway
process - Add memory-optimized primerclip as a separate
align-bwa-trim2
process - Add
workflow-accel-2
workflow
Changed¶
- Improve
PCA
process performance - Use
resolwebio/chipseq:1.1.0
Docker image inmacs14
process - Change formatting of
EFF[*].AA
column insnpeff
process - Save unmapped reads in
aligment-hisat2
process - Turn off test profiling
Fixed¶
- Fix pre-sorting in
upload-master-file
process - Revert
align-bwa-trim
process to use non-memory-optimized primerclip - Fix file processing in
cutadapt-custom-paired
process
6.0.0 - 2017-11-28¶
Added¶
- Add AF filter to amplicon report
- Add number of samples to the output of expression aggregator
- Add
ChIP-Rx
,ChIPmentation
andeClIP
experiment types toreads
descriptor schema - Add
pandas
Python package toresolwebio/latex
Docker image - Add primerclip, samtools, picard-tools and bwa to
resolwebio/dnaseq
Docker image - Add
cufflinks
,RNASeqT
R library,pyarrow
andsklearn
Python packages toresolwebio/rnaseq
Docker image - Add
wigToBigWig
tool toresolwebio/chipseq
Docker image
Changed¶
- BACKWARD INCOMPATIBLE: Drop Python 2 support, require Python 3.4 or 3.5
- BACKWARD INCOMPATIBLE: Make species part of the feature primary key
- BACKWARD INCOMPATIBLE: Substitute Python 2 with Python 3 in
resolwebio/rnaseq
Docker image. The processes to be updated to this version of the Docker image should also have their Python scripts updated to Python 3. - Require Resolwe 5.x
- Set maximum RAM requirement in
bbduk
process - Move Assay type input parameter in RNA-Seq descriptor schema from advanced options to regular options
- Use
resolwebio/rnaseq
Docker image in Cutadapt processes - Use additional adapter trimming option in
cutadapt-custom-single/paired
processes - Show antibody information in
reads
descriptor forChIP-Seq
,ChIPmentation
,ChIP-Rx
,eClIP
,MNase-Seq
,MeDIP-Seq
,RIP-Seq
andChIA-PET
experiment types - Use
resolwebio/dnaseq
Docker image inalign-bwa-trim
process - Refactor
resolwebio/chipseq
Docker image - Use Resolwe’s Test Runner for running tests and add ability to only run a partial test suite based on what proceses have Changed
- Configure Jenkins to only run a partial test suite when testing a pull request
- Make tests use the live Resolwe API host instead of external server
Fixed¶
- Fix merging multiple expressions in DESeq process
- Fix
resolwebio/rnaseq
Docker image’s README - Handle multiple ALT values in amplicon report
- Fix BAM file input in
rsem
process
5.0.1 - 2017-11-14¶
Fixed¶
- Update Features and Mappings ElasticSearch indices building to be compatible with Resolwe 4.0
5.0.0 - 2017-10-25¶
Added¶
- Add automatic headers extractor to
bam-split
process - Add HTML amplicon plot in
coveragebed
process - Add raw RSEM tool output to rsem process output
- Add support for transcript-level differential expression
in
deseq2
process
Changed¶
- BACKWARD INCOMPATIBLE: Bump Django requirement to version 1.11.x
- BACKWARD INCOMPATIBLE: Make
BioProcessTestCase
non-transactional - Require Resolwe 4.x
- Add the advanced options checkbox to the
rna-seq
descriptor schema - Remove static amplicon plot from
coveragebed
andamplicon-report
processes - Update Dockerfile for
resolwebio/latex
with newer syntax and add some additional Python packages
4.2.0 - 2017-10-05¶
Added¶
- Add
resolwebio/base
Docker image based on Ubuntu 17.04 - Add
resolwebio/dnaseq
Docker image - Add
DESeq2
tool toresolwebio/rnaseq
docker image - Add input filename regex validator for
upload-master-file
process
Changed¶
- Remove obsolete mongokey escape functionality
- Report novel splice-site junctions in HISAT2
- Use the latest stable versions of the following bioinformatics
tools in
resolwebio/rnaseq
docker image: Cutadapt 1.14, FastQC 0.11.5, HTSeq 0.9.1, and SAMtools 1.5
4.1.0 - 2017-09-22¶
Added¶
- Add Mus musculus to all BCM workflows’ schemas
- Add
bam-split
process with supporting processesupload-bam-primary
,upload-bam-secondary
andupload-header-sam
Changed¶
- Enable Chemut workflow and process tests
Fixed¶
- Fix chemut
intervals
input option
4.0.0 - 2017-09-14¶
Added¶
- New base and legacy Docker images for processes, which support non-root execution as implemented by Resolwe
Changed¶
- BACKWARD INCOMPATIBLE: Modify all processes to explicitly use the new Docker images
- BACKWARD INCOMPATIBLE: Remove
clustering-hierarchical-genes-etc
process - Require Resolwe 3.x
3.2.0 2017-09-13¶
Added¶
- Add
index-fasta-nucl
andrsem
process - Add custom Cutadapt - STAR - RSEM workflow
3.1.0 2017-09-13¶
Added¶
- Add statistics of logarithmized expressions to
expression-aggregator
- Add input field description to
cutadapt-star-htseq
descriptor schema - Add
HISAT2
andRSEM
tool toresolwebio/rnaseq
docker image
Changed¶
- Remove
eXpress
tool fromresolwebio/rnaseq
docker image - Use system packages of RNA-seq tools in
resolwebio/rnaseq
docker image - Set
hisat2
process’ memory resource requirement to 32GB - Use
resolwebio/rnaseq
docker image inhisat2
process
3.0.0 2017-09-07¶
Added¶
- Add custom Cutadapt - STAR - HT-seq workflow
- Add expression aggregator process
- Add
resolwebio/rnaseq
docker image - Add
resolwebio/latex
docker image - Add access to sample field of data objects in processes via
sample
filter
Changed¶
- BACKWARD INCOMPATIBLE: Remove
threads
input in STAR aligner process and replace it with thecores
resources requirement - BACKWARD INCOMPATIBLE: Allow upload of custom amplicon master files (make
changes to
amplicon-panel
descriptor schema,upload-master-file
andamplicon-report
processes andworkflow-accel
workflow) - BACKWARD INCOMPATIBLE: Remove
threads
input incuffnorm
process and replace it with thecores
resources requirement - Add sample descriptor to
prepare_expression
test function - Prettify amplicon report
Fixed¶
- Fix
upload-expression-star
process to work with arbitrary file names - Fix STAR aligner to work with arbitrary file names
- Fix
cuffnorm
group analysis to work correctly - Do not crop Amplicon report title as this may result in malformed LaTeX command
- Escape LaTeX’s special characters in
make_report.py
tool - Fix validation error in
Test sleep progress
process
2.0.0 2017-08-25¶
Added¶
- Support bioinformatics process test case based on Resolwe’s
TransactionProcessTestCase
- Custom version of Resolwe’s
with_resolwe_host
test decorator which skips the decorated tests on non-Linux systems - Add optimal leaf ordering and simulated annealing to gene and sample hierarchical clustering
- Add
resolwebio/chipseq
docker image and use it in ChIP-Seq processes - Add Odocoileus virginianus texanus (deer) organism to sample descriptor
- Add test for
import-sra
process - Add RNA-seq DSS test
- Add Cutadapt and custom Cutadapt processes
Changed¶
- Require Resolwe 2.0.x
- Update processes to support new input sanitization introduced in Resolwe 2.0.0
- Improve variant table name in amplicon report
- Prepend
api/
to all URL patterns in the Django test project - Set
hisat2
process’ memory resource requirement to 16GB and cores resource requirement to 1 - Filter LoFreq output VCF files to remove overlapping indels
- Add Non-canonical splice sites penalty, Disallow soft clipping and
Report alignments tailored specifically for Cufflinks parameters to
hisat2
process - Remove
threads
input fromcuffquant
andrna-seq
workfows - Set core resource requirement in
cuffquant
process to 1
Fixed¶
- Correctly handle paired-end parameters in
featureCount
- Fix
NaN
in explained variance in PCA. When PC1 alone explained more than 99% of variance, explained variance for PC2 was not returned - Fix input sanitization error in
dss-rna-seq
process - Fix gene source check in hierarchical clustering and PCA
- Enable network access for all import processes
- Fix RNA-seq DSS adapters bug
- Fix sample hierarchical clustering output for a single sample case
1.4.1 2017-07-20¶
Changed¶
- Optionally report all amplicons in Amplicon table
Fixed¶
- Remove remaining references to calling
pip
with--process-dependency-links
argument
1.4.0 2017-07-04¶
Added¶
- Amplicon workflow
- Amplicon descriptor schemas
- Amplicon report generator
- Add Rattus norvegicus organism choice to sample schema
- Transforming form Phred 64 to Phred 33 when uploading fastq reads
- Add primertrim process
- RNA-Seq experiment descriptor schema
- iCount sample and reads descriptor schemas
- iCount demultiplexing and sample annotation
- ICount QC
- Add MM8, RN4 and RN6 options to rose2 process
- Add RN4 and RN6 options to bamplot process
- Archive-samples process
- Add bamliquidator
- CheMut workflow
- Dicty primary analysis descriptor schema
- IGV session to Archive-samples process
- Use Resolwe’s field projection mixins for knowledge base endpoints
amplicon-table
process- Add C. griseus organism choice to Sample descriptor schema
- Add S. tuberosum organism choice to Sample descriptor schema
- Add log2 to gene and sample hierarchical clustering
- Add new inputs to import SRA, add read type selection process
- Set memory resource requirement in jbrowse annotation gff3 and gtf processes to 16GB
- Set memory resource requirement in star alignment and index processes to 32GB
- Add C. elegans organism choice to Sample descriptor schema
- Add D. melanogaster organism choice to Sample descriptor schema
- Set core resource requirement in Bowtie process to 1
- Set memory resource requirement in amplicon BWA trim process to 32GB
- Add new master file choices to amplicon panel descriptor schema
- Add S. tuberosum organism choice to RNA-seq workflow
- Add Cutadapt process
- Add leaf ordering to gene and sample hierarchical clustering
Fixed¶
- Use new import paths in
resolwe.flow
- Upload reads (paired/single) containing whitespace in the file name
- Fix reads filtering processes for cases where input read file names contain whitespace
- Add additional filtering option to STAR aligner
- Fix bbduk-star-htseq_count workflow
- Fix cuffnorm process: Use sample names as labels (boxplot, tables), remove group labels input, auto assign group labels, add outputs for Rscript output files which were only available compressed
- Derive output filenames in hisat2 from the first reads filename
- Correctly fetch KB features in
goea.py
- Append JBrowse tracks to sample
- Replace the BAM MD tag in align-bwa-trim process to correct for an issue with the primerclip tool
- Fix typo in trimmomatic and bbduk processes
- Use re-import in etc and hmmer_database processes
Changed¶
- Support Resolwe test framework
- Run tests in parallel with Tox
- Use Resolwe’s new
FLOW_DOCKER_COMMAND
setting in test project - Always run Tox’s
docs
,linters
andpackaging
environments with Python 3 - Add
extra
Tox testing environment with a check that there are no large test files inresolwe_bio/tests/files
- Replace Travis CI with Genialis’ Jenkins for running the tests
- Store compressed and uncompressed .fasta files in
data:genome:fasta
objects - Change sample_geo descriptor schema to have strain option available for all organisms
- More readable rna-seq-quantseq schema, field stranded
- Remove obsolete Gene Info processes
- Change log2(fc) default from 2 to 1 in diffexp descriptor schema
- Change Efective genome size values to actual values in macs14 process
- Change variable names in bowtie processes
- Remove iClip processes, tools, files and tests
1.3.0 2017-01-28¶
Changed¶
- Add option to save expression JSON to file before saving it to Storage
- Update
upload-expression
process - No longer treat
resolwe_bio/tools
as a Python package - Move processes’ test files to the
resolwe_bio/tests/files
directory to generalize and simplify handling of tests’ files - Update differential expression (DE) processors
- Update
generate_diffexpr_cuffdiff
django-admin command - Save gene_id source to
output.source
for DE, expression and related objects - Refactor
upload-diffexp
processor - Update sample descriptor schema
- Remove obsolete descriptor schemas
- Add stitch parameter to rose2 processor
- Add filtering to DESeq2
- Set Docker Compose’s project name to
resolwebio
to avoid name clashes - GO enrichment analysis: map features using gene Knowledge base
- Add option to upload .gff v2 files with upload-gtf processor
- Replace Haystack with Resolwe Elastic Search API
- Require Resolwe 1.4.1+
- Update processes to be compatible with Resolwe 1.4.0
Added¶
- Process definition documentation style and text improvements
- Add
resolwe_bio.kb
app, Resolwe Bioinformatics Knowledge Base - Add tests to ensure generators produce the same results
- Upload Gene sets (
data:geneset
) - Add
generate_geneset
django-admin command - Add
generate_diffexpr_deseq
django-admin command - Add ‘Generate GO gene sets’ processor
- Add generic file upload processors
- Add upload processor for common image file types (.jpg/.tiff/.png/.gif)
- Add upload processor for tabular file formats (.tab/.tsv/.csv/.txt/.xls/.xlsx)
- Add Trimmomatic process
- Add featureCounts process
- Add Subread process
- Add process for hierarchical clusteing of samples
- Add gff3 to gtf file converter
- Add microarray data descriptor schema
- Add process for differential expression edgeR
BioCollectionFilter
andBidDataFilter
to support filtering collections and data by samples on API- Added processes for automatically downloading single and paired end SRA files from NCBI and converting them to FASTQ
- Added process for automatically downloading SRA files from NCBI and converting them to FASTQ
- Add HEAT-Seq pipeline tools
- Add HEAT-Seq workflow
- Add
create-geneset
,create-geneset-venn
processors - Add
source
filter to feature search endpoint - Add bamplot process
- Add gene hiererhical clustering
- Add cuffquant workflow
- Support Django 1.10 and versionfield 0.5.0
- django-admin commands
insert_features
andinsert_mappings
for importing features and mappings to the Knowledge Base - Add bsmap and mcall to analyse WGBS data
- Vaccinesurvey sample descriptor schema
- Add RNA-Seq single and paired-end workflow
Fixed¶
- Set
presample
toFalse
for Samples created on Sample endpoint - Fix FastQC report paths in processors
- Fix
htseq_count
andfeatureCounts
for large files - Fix
upload gtf annotation
- Fix gene_id field type for differential expression storage objects
- Order data objects in
SampleViewSet
- Fix sample hiererhical clustering
- Fix name in gff to gtf process
- Fix clustering to read expressed genes as strings
- Fix protocol labels in
rna-seq-quantseq
descriptor schema
1.2.0 2016-07-27¶
Changed¶
- Decorate all tests that currently fail on Docker with
skipDockerFailure
- Require Resolwe’s
master
git branch - Put packaging tests in a separate Tox testing environment
- Rename DB user in test project
- Change PostgreSQL port in test project
- Add ROSE2 results parser
- Compute index for HISAT2 aligner on genome upload
- Updated Cuffquant/Cuffnorm tools
- Change ROSE2 enhancer rank plot labels
- Refactor processor syntax
- Move processes tests into
processes
subdirectory - Split
sample
API endpoint tosample
for annotatedSamples
andpresample
for unannotatedSamples
- Rename test project’s data and upload directories to
.test_data
and.test_upload
- Save fastq files to
lists:basic:file
field. Refactor related processors. - Reference genome-index path when running aligners.
- Add pre-computed genome-index files when uploading reference fasta file.
- Include all necessary files for running the tests in source distribution
- Exclude tests from built/installed version of the package
- Move testing utilities from
resolwe_bio.tests.processes.utils
toresolwe_bio.utils.test
- Update Cuffdiff processor inputs and results table parsing
- Refactor processes to use the updated
resolwe.flow.executors.run
command - Refactor STAR aligner - export expressions as separate objects
Fixed¶
- Make Tox configuration more robust to different developer environments
- Set
required: false
in processor input/output fields where necessary - Add
Sample
‘sData objects
toCollection
whenSample
is added - Fixed/renamed Cufflinks processor field names
Added¶
skipDockerFailure
test decorator- Expand documentation on running tests
- Use Travis CI to run the tests
- Add
Sample
model and corresponding viewset and filter - Add docker-compose command for PostgreSQL
- API endpoint for adding
Samples
toCollections
- HISAT2 aligner
- Use Git Large File Storage (LFS) for large test files
- Test for
generate_samples
django-admin command - django-admin command:
generate_diffexpr
1.1.0 2016-04-18¶
Changed¶
- Remove obsolete utilities superseded by resolwe-runtime-utils
- Require Resolwe 1.1.0
Fixed¶
- Update sample descriptor schema
- Include all source files and supplementary package data in sdist
Added¶
flow_collection: sample
to processes- MACS14 processor
- Initial Tox configuration for running the tests
- Tox tests for ensuring high-quality Python packaging
- ROSE2 processor
- django-admin command:
generate_samples
1.0.0 2016-03-31¶
Changed¶
- Renamed assertFileExist to assertFileExists
- Restructured processes folder hierarchy
- Removed re-require and hard-coded tools’ paths
Fixed¶
- Different line endings are correctly handled when opening gzipped files
- Fail gracefully if the field does not exist in assertFileExists
- Enabled processor tests (GO, Expression, Variant Calling)
- Enabled processor test (Upload reads with old Illumina QC encoding)
- Made Resolwe Bioinformatics work with Resolwe and Docker
Added¶
- Import expressions from tranSMART
- Limma differential expression (tranSMART)
- VC filtering tool (Chemical mutagenesis)
- Additional analysis options to Abyss assembler
- API endpoint for Sample
- Initial documentation